[Bioperl-l] Locuslink?? Help

[Hilmar Lapp]

In the absence of any better answer from someone else, here is mine: 
you can't get the LocusLink entry through DB::GenBank. In fact, there 
is no remote DB interface for retrieving LL entries yet - you or 
anybody else is welcome to write that though (the framework for setting 
up the connection etc should all be there to inherit from).

Instead, download LL to your computer, then ... uuhhm, well I'm afraid 
Bio::Index::* doesn't support LL either.

So, either you write the Bio::Index module that support LL, or you dump 
LL into biosql and then write a tool that extracts it based on protein 
dbxref.

Bottom line: I wish there was but I'm afraid there isn't an easy way to 
do this yet in Bioperl.

	-hilmar

On Thursday, May 15, 2003, at 11:48  AM, Eric Wang wrote:

> Dear all,
>
> I have on my hand a protein name and I want to access the locus link
> information and the NT_ contig information.
> I tried several times with Bio::DB::GenBank objects but seems like I 
> could
> only obtain the sequence but not the LL data.  So I guess my question 
> is
> how would I go about finding the LocusLink information for this 
> protein?
>
> Thanks for all the help!!
>
> Eric
>
>  On Wed, 14 May 2003, Hilmar Lapp wrote:
>
>> Are you talking about querying Genbank at NCBI through a
>> Bio::DB::GenPept object? I don't understand what exactly you're trying
>> to do. The LL parser in bioperl is a stream parser, not a random 
>> access
>> interface.
>>
>> My recommendation is to state what you are trying to achieve, paste in
>> the script or the part that supposedly does this, and send that to the
>> list. There's many more very knowledgeable people there ... who may
>> have even tried to do the same as you before.
>>
>> 	-hilmar
>>
>> On Wednesday, May 14, 2003, at 10:46  PM, Eric Wang wrote:
>>
>>> Thanks for your help.
>>> I am still confused on how to query locuslink for the tags
>>> I have on my hand just the protein name and I want to basically find
>>> the
>>> intron/exon boundaries.
>>> But it seems like when I use get_stream_by_query('prot_name'), I got
>>> nothing... do you know a better way to approaching the problem?
>>>
>>> Thanks
>>> Eric
>>>
>>> On Wed, 14 May 2003, Hilmar Lapp wrote:
>>>
>>>> Theoretically yes, but be aware that these might be huge. If you 
>>>> fetch
>>>> them remotely, you don't do a favor to anyone, not to NCBI and not 
>>>> to
>>>> yourself. You want to have a local indexed flat file download for
>>>> that.
>>>>
>>>> 	-hilmar
>>>>
>>>> On Wednesday, May 14, 2003, at 08:40  PM, Eric Wang wrote:
>>>>
>>>>> Thanks for your help!
>>>>> Yeah, I noticed there isn't any top_features but
>>>>> the annotations will contain reference sequence (NT_ contigs) ?
>>>>> if that's the case, I would just use get_seq_by_id to retrieve it
>>>>> right?
>>>>>
>>>>>
>>>>>
>>>>> Thanks again
>>>>>
>>>>> Eric
>>>>> On Wed, 14 May 2003, Hilmar Lapp wrote:
>>>>>
>>>>>> my $seqio = Bio::SeqIO->new(-format => "locuslink");
>>>>>> while(my $ll = $seqio->next_seq()) {
>>>>>> 	# whatever
>>>>>> }
>>>>>>
>>>>>> There won't be any sequence features though. LL essentially is 
>>>>>> lots
>>>>>> of
>>>>>> tag/value pairs, and that is how it ends up (i.e.,
>>>>>> $ll->annotation->get_Annotations()).
>>>>>>
>>>>>> The locus-contains-splice variants thing in LL isn't properly
>>>>>> reflected
>>>>>> in the resulting SeqI object, which is a problem of the Bioperl
>>>>>> object
>>>>>> model in the first place (there is no good object right now that
>>>>>> would
>>>>>> properly reflect an LL object wrt the datatype). What you'd want 
>>>>>> is
>>>>>> a
>>>>>> gene model. Maybe it's worth thinking whether the feature-driven
>>>>>> SeqFeature::Gene::* objects fit the bill here. I'm not convinced 
>>>>>> yet
>>>>>> though.
>>>>>>
>>>>>> 	-hilmar
>>>>>>
>>>>>> On Wednesday, May 14, 2003, at 05:44  PM, Eric Wang wrote:
>>>>>>
>>>>>>> I have a question regarding how to retrieve locuslink objects.
>>>>>>> I searched the documentation everywhere and couldn't find it.
>>>>>>> Can anybody give me some pointers on how to retrieve locuslink
>>>>>>> objects
>>>>>>> and
>>>>>>> can I use the top_Seqfeatures() for this object?
>>>>>>>
>>>>>>> Thanks in advance
>>>>>>>
>>>>>>> Eric
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioperl-l mailing list
>>>>>>> Bioperl-l at bioperl.org
>>>>>>> http://pw600a.bioperl.org/mailman/listinfo/bioperl-l
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------